seqfile = seq.tmp
outfile = results
icode = 0
noisy = 0
verbose = 0
runmode = -2
seqtype = 1
CodonFreq = 2
aaDist = 0
model = 0
NSsites = 0
Mgene = 0
fix_omega = 0
omega = .4
fix_alpha = 0
alpha = 0.
Malpha = 0
ncatG = 8
clock = 0
getSE = 1
RateAncestor = 1
Small_Diff = .5e-6
cleandata = 1
method = 0
fix_kappa = 0
kappa = 2
